Contacts of the helix formed by residues 182 - 192 (chain B) in PDB entry 3GTU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 182 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP 3.9 5.1 - - - +
180B GLU 3.5 9.0 - - - +
181B PHE* 1.4 86.9 - - - +
183B ASN* 1.3 62.2 + - + +
184B LEU 3.4 0.2 - - - -
185B LYS* 3.6 24.0 - - - +
186B ALA* 3.3 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B SER* 2.9 44.8 + - - +
145B LEU* 3.8 15.2 - - - +
146B GLY* 3.0 32.6 + - - +
148B PHE 5.2 1.2 - - - +
181B PHE* 2.8 2.0 + - - -
182B PRO* 1.3 81.1 - - + +
184B LEU* 1.3 64.1 + - - +
186B ALA* 3.4 8.0 + - - +
187B PHE* 3.3 17.2 + - - +
190B ARG* 5.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 3.8 43.7 - - + +
141B PHE* 4.1 3.4 - - + -
142B SER* 4.0 23.6 - - - +
145B LEU* 4.2 7.0 - - + -
151B PHE* 4.1 25.4 - - + -
167B LEU* 4.2 17.0 - - + -
178B LEU* 4.3 15.3 - - + -
181B PHE* 2.9 24.5 + - + +
183B ASN* 1.3 77.5 - - - +
185B LYS* 1.3 61.0 + - - +
187B PHE* 2.8 23.9 + - + +
188B MET* 3.0 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.5 34.5 - - + +
179B ASP* 3.4 35.2 + - - +
181B PHE 3.3 0.8 + - - +
182B PRO* 3.6 28.5 - - - +
183B ASN 3.4 0.2 - - - -
184B LEU* 1.3 76.7 - - - +
186B ALA* 1.3 61.4 + - - +
188B MET* 3.5 10.2 + - - +
189B CYS* 3.3 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO 3.3 12.2 + - - +
183B ASN* 3.6 10.8 - - - +
184B LEU 3.1 1.0 - - - -
185B LYS* 1.3 75.8 - - - +
187B PHE* 1.3 66.8 + - - +
189B CYS* 3.5 6.3 + - - +
190B ARG* 3.0 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.0 9.9 - - + -
149B SER 4.0 8.3 - - - -
150B TRP* 3.6 25.6 - + - -
151B PHE* 3.9 30.1 - + - -
160B ASP* 3.5 44.6 - - + -
164B TYR* 4.0 28.7 - + + -
167B LEU* 4.1 9.9 - - + -
183B ASN 3.3 6.7 + - - +
184B LEU* 2.8 14.6 + - - +
186B ALA* 1.3 79.3 - - - +
188B MET* 1.3 68.7 + - - -
190B ARG* 3.2 17.7 + - - +
191B PHE* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TYR* 3.7 20.4 - - + +
167B LEU* 3.6 23.3 - - + +
168B ASP* 3.4 33.2 - - - +
171B ARG* 3.2 39.7 - - - +
178B LEU* 3.8 18.6 - - + -
184B LEU 3.0 14.2 + - - +
185B LYS* 3.7 7.9 - - - +
186B ALA 3.4 0.2 - - - -
187B PHE* 1.3 88.5 - - - +
189B CYS* 1.3 58.5 + - - +
191B PHE* 3.4 3.4 + - - +
192B GLU* 2.9 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LYS* 3.3 17.1 + - - +
186B ALA* 3.8 8.3 - - - +
188B MET* 1.3 78.9 - - - +
190B ARG* 1.3 58.5 + - - +
192B GLU* 3.3 7.8 + - - +
193B ALA* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.9 3.6 - - - +
148B PHE 4.1 5.3 + - - -
149B SER* 2.8 46.8 + - - +
150B TRP* 3.5 22.5 - - + -
183B ASN 5.0 1.0 + - - -
186B ALA* 3.0 42.2 + - - +
187B PHE* 3.4 27.2 - - - +
189B CYS* 1.3 77.5 - - - +
191B PHE* 1.3 61.1 + - - +
193B ALA* 3.5 15.1 + - - +
194B LEU* 3.7 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.3 4.3 - - + -
150B TRP* 4.2 16.8 - + + -
156B LEU* 4.8 1.6 - - + -
160B ASP* 4.5 7.4 - - + -
161B PHE* 3.5 57.2 - + - -
164B TYR* 3.3 55.6 - + + -
187B PHE* 2.9 21.6 + + + +
188B MET 3.7 4.0 - - - +
190B ARG* 1.3 72.7 - - - +
192B GLU* 1.3 61.6 + - - +
193B ALA 3.0 5.1 + - - -
194B LEU* 3.2 37.5 + - + +
197B ILE* 3.6 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TYR* 3.2 33.6 + - + +
171B ARG* 3.0 34.9 + - - -
188B MET* 2.9 24.7 + - - +
189B CYS* 4.0 6.8 + - - +
191B PHE* 1.3 73.6 - - + +
193B ALA* 1.3 60.7 + - - +
194B LEU 3.2 0.4 - - - -
197B ILE* 4.1 8.1 - - - -
198B ALA* 3.3 27.2 - - - +
201B LEU* 3.6 16.4 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il